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Results from 3 yr of hydrographic time series are shown for Willapa Bay, Washington, a macrotidal, partially mixed estuary whose river and ocean end members are both highly variable. Fluctuating ocean conditionsalternations between wind-driven upwelling and downwelling, and intrusions of the buoyant Columbia River plume-are shown to force order-of-magnitude changes in salinity gradients on the event (2-10 day) scale. An effective horizontal diffusivity parameterizing all up-estuary salt flux is calculated as a function of riverflow: results show that Willapa's volume-integrated salt balance is almost always far from equilibrium. At very high riverflows (the top 15% of observations) the estuary loses salt, on average, while at all other riverflow levels it gains salt. Under summer, low-riverflow conditions, in fact, the effective diffusivity K is large enough to drive a net increase in salinity that is 3-6 times the seaward, river-driven salt flux. This diffusion process is amplified, not damped, by increased tidal forcing, contrary to the expectation for baroclinic exchange. Furthermore, K varies along the length of the estuary as ϳ5% of the rms tidal velocity times channel width, a scaling consistent with density-independent stirring by tidal residuals. To summarize Willapa's event-and seasonal-scale variability, a simple diagnostic parameter space for unsteady estuarine salt balances is presented, a generalization from the Hansen and Rattray steady-state scheme.

A realistic hindcast simulation of the Salish Sea, which encompasses the estuarine systems of Puget Sound, the Strait of Juan de Fuca, and the Strait of Georgia, is described for the year 2006. The model shows moderate skill when compared against hydrographic, velocity, and sea surface height observations over tidal and subtidal time scales. Analysis of the velocity and salinity fields allows the structure and variability of the exchange flow to be estimated for the first time from the shelf into the farthest reaches of Puget Sound. This study utilizes the total exchange flow formalism that calculates volume transports and salt fluxes in an isohaline framework, which is then compared to previous estimates of exchange flow in the region. From this analysis, residence time distributions are estimated for Puget Sound and its major basins and are found to be markedly shorter than previous estimates. The difference arises from the ability of the model and the isohaline method for flux calculations to more accurately estimate the exchange flow. In addition, evidence is found to support the previously observed spring-neap modulation of stratification at the Admiralty Inlet sill. However, the exchange flow calculated increases at spring tides, exactly opposite to the conclusion reached from an Eulerian average of observations.

Harmful algal blooms (HABs) pose a significant threat to human and marine organism health, and negatively impact coastal economies around the world. An improved understanding of HAB formation and transport is required to improve forecasting skill. A realistic numerical simulation of the US Pacific Northwest region is used to investigate transport pathways from known HAB formation hot spots, specifically for Pseudo-nitzschia (Pn), to the coast. We show that transport pathways are seasonal, with transport to the Washington (WA) coast from a northern source (the Juan de Fuca Eddy) during the summer/fall upwelling season and from a southern source (Heceta Bank) during the winter/early spring due to the predominant wind-driven currents. Interannual variability in transport from the northern source is related to the degree of wind intermittency with more transport during years with more frequent relaxation/downwelling events. The Columbia River plume acts to mitigate transport to the coast as the plume front blocks onshore transport. The plume's influence on alongshore transport is variable although critical in aiding transport from the southern source to the WA coast via plume entrainment. Overall transport from our simulations captures most observed Pn HAB beach events from 2004 to 2007 (characterized by Pseudo-nitzschia cell abundance); however, numerous false positives occur. We show that incorporating phytoplankton biomass results from a coupled biogeochemical model reduces the number of false positives significantly and thus improves our Pn HAB predictions.